One of the most powerful and most useful modules on Drupal is Views. With one screen you can build custom pages & blocks based around your content, select the exact fields you need, add filters and arguments, and relatively easily customize the display, and that's just scratching the surface. In fact, Views is so flexible that I've built sites which have 90% of their architecture based solely around taxonomies and Views.
The main trick to making using Views manageable is to save them out as files and load them through a module. It sounds really easy, and it is really, but there's a few steps to it.
The first step is to have a per-site module specially for holding these kinds of things, a general bucket for your random chaos.

The second step is to go to each View in turn and export it to a file in your new module's directory. To do that, go to your site's Views list page and for each of the custom ones you've built or modified, click the Export link next to it to bring you to a page with the view's code listed out:
What you need to do next is save this text out to a file. By default all of the text is selected, but you're not ready for that yet. You first need to create the file to store the text. I like to use the following filename structure:
view.[viewname].inc
This both groups all views together and makes them easy to identify at a quick glance. Going by this, the above view would be saved with the filename:
view.taxonomy_term.inc
Now, just copy all of the code from the Export page into the newly created file. Simple, huh? Well, there's a little gotcha - you need to add "<?php" to the top of the file otherwise the next steps won't work right, e.g.:

Well, we're not done yet, we still have to tell the site that there are views in this new module. This involves two further steps..
The first part is to tell the system that this module uses the Views API by adding some lines to your module:

The last part is to load the views into the system. To do this you must add another file to your module directory named:
[modulename].views_default.inc
Then add the following to the file:

And now you're done!
Well, almost. Your site is still going to load the view that's already in your database rather than the one in your module. To fix this just go back to the main Views list page, find the view you just exported and click the "Revert" link to revert it from the database-stored version to what was in your file; don't be afraid when it says "Are you sure you want to revert the view?" because yes, that's what you want to do. So do it.
And now you really are done. Enjoy. And make sure you save it into your site's SVN server promptly.
Learning Exercise:
To make more of this, and to test your PHP skills, try changing funkychicken_views_default_views() to automatically load all files named 'view.[something].inc' instead of having to manually list each one.